Difference between revisions of "Main Page"

	Included in psico; This command or function is available from psico, which is a PyMOL extension.
Module	psico.fitting

Latest revision as of 12:54, 12 March 2024

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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org

Quick Links
Tutorials	Table of Contents	Commands
Script Library	Plugins	FAQ
Gallery \| Covers	PyMOL Cheat Sheet (PDF)	Getting Help

News & Updates
Official Release	PyMOL v3.0 has been released on March 12, 2024.
New Plugin	CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models
Official Release	PyMOL v2.5 has been released on May 10, 2021.
Python 3	New Python 3 compatibility guide for scripts and plugins
POSF	New PyMOL fellowship announced for 2022-2023
Tutorial	Plugins Tutorial updated for PyQt5
New Plugin	PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
Selection keywords	New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update	MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script	dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News	See Older News.

Did you know...

Theseus

theseus is a wrapper for the theseus program for maximum likelihood superpositioning of macromolecular structures. It produces results very similar to xfit.

Installation

For Linux and macOS, all dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c schrodinger theseus

Usage

Superpose two objects:

theseus mobile, target [, match [, cov [, cycles [, mobile_state [, target_state [, exe [, preserve ]]]]]]]

Ensemble-fit states of a multi-state object:

intra_theseus selection [, state [, cov [, cycles [, exe [, preserve ]]]]]

Arguments

mobile = string: atom selection for mobile atoms
target = string: atom selection for target atoms
match = string: in, like, align, none or the name of an alignment object (see local_rms help for details) {default: align}
cov = 0/1: 0 is variance ..→

A Random PyMOL-generated Cover. See Covers.

@@ Line 1: / Line 1: @@
 __NOTOC__
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-|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
+|+ style="font-size: 1.0em; font-weight: normal; color: #FFFFFF; text-align:right; background: #B22222; padding-top:0.5em; padding-bottom: 0.25em; padding-right: 0.60em; border-top: 2px solid #B22222; border-bottom: 1px solid #fff;" |hosted by [[File:SBGridlogo2.jpg|140 px|link=https://sbgrid.org/]]
-|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
+|}
+{| align="center" style="padding-bottom: 3em;"
+|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
+|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
 | The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
-|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
+|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
-| New accounts: email jason (dot) vertrees (@) gmail dot com
+| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
-|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
+|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
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+{| align="center" width="45%" style="background: #FFFFFF; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
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 |-
-| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
+| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
 |-
-| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
+| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
 |-
-| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
+| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
 ||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
-||'''[[GoogleSearch]]'''
+||'''[[PyMOL_mailing_list|Getting Help]]'''
 |}
@@ Line 25: / Line 29: @@
 |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
 |-
-! Tips & Tricks
+! Official Release
-| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
+| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
-|-
-|-
-! New Script
-| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.
-|-
-! New Script
-| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
-|-
-! New Script
-| [[DistancesRH|Distances RH]]
-|-
-! PyMOL on the iPad
-| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.
-|-
-! OS X Compatibility
-| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].
-|-
-! New Script
-| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
-|-
-! New Script
-| [[b2transparency]] can set surface transparency based on atom b-factor
-|-
-! New Extension
-| [[psico]] is a python module which extends PyMOL with many commands
-|-
-! New Script
-| [[uniprot_features]] makes named selections for sequence annotations from uniprot
 |-
 ! New Plugin
-| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
+| [[CavitOmiX|CavitOmiX]] calculate [https://innophore.com Catalophore™ cavities], predict protein structures with [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold by NVIDIA-BioNeMo], [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold] and retrieve [https://www.deepmind.com/research/highlighted-research/alphafold Alphafold] models
 |-
-! New Script
+! Official Release
-| [[set_phipsi]] can set phi/psi angles for all residues in a selection
+| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 |-
-! New Script
+! Python 3
-| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack.
+| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 |-
-! New Script
+! POSF
-| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
+| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 |-
-! New Script
+! Tutorial
-| [[cyspka]] is an experimental surface cysteine pKa predictor.
+| [[Plugins Tutorial]] updated for PyQt5
 |-
 ! New Plugin
-| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map
+| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
-|-
-! New Script
-| [[spectrum_states]] colors states of multi-state object
-|-
-! New Script
-| [[TMalign]] is a wrapper for the TMalign program
-|-
-! Gallery Updates
-| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
-|-
-! New Script
-| [[save_settings]] can dump all changed settings to a file
 |-
-! Tips & Tricks
+! Selection keywords
-| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
+| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 |-
-! Wiki Update
+! Plugin Update
-| Wiki has been updated. Please report any problems to the sysops.
+| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
-|-
-! New Scripts
-| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
 |-
 ! New Script
-| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
+| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
-|-
-! New Script
-| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]].
-|-
-! New Script
-| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
 |-
 ! Older News
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